Microbial fuel cells equipped with SPEEK-MEA (SPEEK-MFC) and Nafion-MEA (Nafion-MFC) were constructed with organic waste as electron donor and lake sediment as inoculum and were then evaluated comprehensively by electrochemical and microbial analyses. The proton conductivity of SPEEK was several hundreds-fold lower than that of Nafion 117, whereas the oxygen mass and diffusion transfer coefficients of SPEEK were 10-fold lower than those of Nafion 117. It was difficult to predict which was better membrane for MFC based on the feature of membrane. Analyses of polarization curves indicated that the potential of electricity production was similar in both MFCs, as the SPEEK-MFC produced 50–80% of the practical current density generated by the Nafion-MFC. Chronopotentiometry analyses indicated that the Nafion-MEA kept the performance longer than the SPEEK-MEA for long period, whereas performance of both anodes improved on time. Multidimensional scaling analyses based on DGGE profiles revealed the anolytic and biofilm communities of the SPEEK-MFC had developed differently from those of the Nafion-MFC. Clone library analyses indicated that Geobacter spp. represented 6.3% of the biofilm bacterial community in the Nafion-MFC but not detected in the SPEEK-MFC. Interestingly, the clone closely related to Acetobacterium malicum strain HAAP-1, belonging to the homoacetogens, became dominant in both anolytic and biofilm communities of the SPEEK-MFC. It was suggested that the lower proton conductivity of SPEEK-MEA allowed the bacteria closely related to strain HAAP-1 to be dominant specifically in SPEEK-MFC. These results indicated that Nafion-MFC ranked with SPEEK-MFC and that MEAs had strong selective pressure for electricity-producing bacterial community.